1. Field of the Invention
The present invention relates generally to the field of devices for performing detection reactions involving biomolecules. In particular, the invention relates to devices for processing microarray slides used in such detection reactions. More specifically, the invention relates to a novel device for interfacing with a microarray slide to provide for the controlled delivery of fluids to selected regions of the slide surface as well as an instrument for performing simultaneous processing of a plurality of microarray slides, each used in combination with an interface device according to the invention.
2. Description of Related Art
A variety of biological and chemical assays have been developed for detecting the presence of compounds of interest in samples. In the biomedical field, methods for detecting the presence of specific nucleotide sequences, proteins or peptides are utilized, for example, in diagnosing various medical conditions, determining predisposition of patients to diseases, and performing DNA fingerprinting.
In general, biological and chemical assays are based on exposing an unknown sample to one or more known reactants and monitoring the progress or measuring the outcome of the reaction. It is often desirable to expose a sample to multiple reactants, to react multiple dilutions of a single sample with one or multiple reactants, to expose multiple samples to a single reactant, or to perform multiple repetitions of a particular assay for a given sample, in order to improve reliability. There is currently a high level of interest in the development of high throughput methods for performing multiple biological and chemical analyses of this type simultaneously, quickly, and conveniently.
One recently developed method for performing multiple chemical reactions simultaneously is to form a microarray of multiple spots of reactant molecules on a planar substrate such as a glass microscope slide, typically in a two-dimensional grid pattern, and apply liquid reagents and reactants to the slide to contact multiple spots simultaneously. Various reaction steps may be preformed with the bound molecules in the microarray, including exposure of bound reactant molecules to liquid reagents or reactants, washing, and incubation steps. The progress or outcome of the reaction (or other association between bound molecules and reagents which is not truly a reaction) may be monitored at each spot in the microarray in order to characterize either material(s) immobilized on the slide or material(s) in a liquid sample. Although it is typical to immobilize known reactants on the substrate and expose an unknown liquid sample (e.g., a “probe solution”) to the immobilized reactants and monitor the reaction between the sample and the various reactants in order to characterize the sample, it is also possible to immobilize one or more unknown samples on the substrate and expose them to a liquid containing one or more known reactants.
Microarrays are frequently used in analysis of DNA samples, but may also be used in diagnostic testing of other types of patient samples. Spots in microarrays may be formed of various large biomolecules, such as DNA, RNA, and proteins, smaller molecules such as drugs, co-factors, signaling molecules, peptides or oligonucleotides. Cultured cells may also be grown onto microarrays. As an example, if it is desired to detect the presence of particular DNA sequences in a patient sample, the sample is exposed to a microarray of spots formed of oligonucleotides having sequences complementary to sequences of interest. If the DNA sequence of interest is present in a patient sample, it will hybridize with the bound oligonucleotides. The occurrence of hybridization at a particular spot then indicates the presence of the sequence associated with that spot in the sample. Hybridization can be detected by various methods, many of which give indication of the quantity, as well as presence, of sequences of interest in the sample. One commonly used method involves labeling the sample with a fluorescent dye so that fluorescence can be detected at spots where hybridization occurred. Various types of slide readers are commercially available for reading microarray slides.
Microarrays offer great potential for performing complex analyses of samples by carrying out multiple detection reactions simultaneously. However, a current limitation of microarrays is the time and care required to process slides to obtain reliably high quality results. The need for high quality processing is particularly pronounced because individual microarrays slides are expensive and only limited quantities of the samples used in the reactions may be available, making it particularly important to obtain good results consistently.
Both manual and automated methods of processing microarrays have been developed. However, to date, no method has been completely satisfactory. In order to process a microarray manually, at certain reaction steps the appropriate reagent or reactant solution is applied to the microarray slide and a cover slip applied to spread the solution out into a thin layer that covers the entire microarray and prevents evaporation. Washing steps are typically carried out by placing slides in jars of wash solution. Each processing step must be carried out by hand, necessitating a large amount of human effort. Moreover, the success of the procedure is largely dependent on the skill of the human technician. A single technician is typically able to process at most only 10-15 slides per day. An additional drawback of manual processing techniques is that an essentially open system is used, presenting a high potential for evaporation, spilling or leakage of samples or reagents. If microarray slides are allowed to dry out, data quality will be compromised. Leakage and spilling can be a significant problem, in that certain samples or reagents may be hazardous, and also because leakage or spilling of genetic material, even in minute amounts, can contaminate other samples being processed in the lab and lead to erroneous results.
Various methods have been developed to overcome the limitations of manual slide processing. These range from simple slide processing chambers designed to simplify the application of solutions to microarray slides and reduce evaporation and leakage of solutions, to large and expensive machines capable of processing large numbers of slides simultaneously.
Loeffler et al. (PCT publication WO 00/63670, dated Oct. 26, 2000 describe a slide processing chamber designed for processing microarray slides. Freeman (U.S. Pat. No. 5,958,760, issued Sep. 28, 1999 Stapleton et al. (U.S. Pat. No. 5,922,604 issued Jul. 13, 1999 Stevens et al. (U.S. Pat. No. 5,605,813, issued Feb. 25, 1997 and Richardson (U.S. Pat. No. 6,052,224, issued Apr. 18, 2000 all disclose slide processing chambers not specifically disclosed for use in microarray processing, but which serve to illustrate the general state of the art relating to the processing of individual slides.
Devices capable of processing multiple slides simultaneously in an automated fashion are described by Custance (U.S. Pat. No. 6,238,910, issued May 29, 2001 and Juncosa et al. (U.S. Pat. No. 6,225,109, issued May 1, 2001).
All of the above mentioned patents or applications are incorporated herein by reference.
Devices for automated processing of microarray slides offer many advantages, but are prohibitively expensive for labs that do not need to process large numbers of slides. In addition, even with improved reproducibility delivered by automation, the results obtained with commercially available instruments of this type frequently do not meet the high quality and consistency standards that are desirable, particularly because of the cost of microarray slides and the often limited availability of samples.
With increased interest and development effort in the field of microarrays, equipment used to manufacture microarrays on slides has been developed which allows for the formation of arrays with higher spot densities and smaller individual spot sizes. At the same time, detection equipment used with microarrays is becoming capable of detecting smaller spots at higher densities. However, some tests are best performed with a number of spots less than the total number that can be formed on a slide. It would be desirable to exploit the higher spot density and higher density detection capability by performing several such tests simultaneously on a single slide, essentially breaking one large high density array into a number of smaller arrays. It would thus be advantageous to have a method of interfacing to a microarray which would permit selective access to portions of a microarray.
There remains a need for a method of interfacing to microarray slides which eliminates or minimizes leakage or spillage, provides reliable, reproducible results, requires minimal volumes of samples and reagents, and can be used conveniently for manual processing of small numbers of slides but may also be adapted to automated slide processing for handling larger numbers of slides.